If you want Tot's window to float above other windows on the Mac desktop, use the "Display as Floating Window" item in the Window menu.
 

Note that the Window menu is only visible when you're using Tot with a Dock icon. You'll need to turn off the menu bar icon temporarily to change it.
 

If this is something you want to change regularly, you can manually setup a keyboard shortcut to perform the action. You can use that shortcut in the menu bar mode.
 

https://support.iconfactory.com/kb/tot/keyboard-shortcuts-in-tot